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Crystal structure of human PCNA in complex with three p15 peptides
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VYM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 291 28% PEG 400, 0.2 M CaCl2, 0.1 M Hepes
Crystal Properties Matthews coefficient Solvent content 2.92 57.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.24 α = 90 b = 89.75 β = 117.25 c = 85.13 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 2M 2017-10-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.00 ELETTRA 5.2R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.9 89.75 92.2 0.105 0.986 4.77 1.768 42698 90.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3.08 91.3 0.763 0.73 1.762
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1VYM 2.9 75.69 22217 1097 98.43 0.203 0.2 0.2146 0.2632 0.2675 RANDOM 98.238
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 6.71 5.99 -5.61 -4.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_3_deg 20.187 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_1_deg 8.159 r_angle_refined_deg 2.396 r_angle_other_deg 1.274 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.189 r_dihedral_angle_3_deg 20.187 r_dihedral_angle_4_deg 18.941 r_dihedral_angle_1_deg 8.159 r_angle_refined_deg 2.396 r_angle_other_deg 1.274 r_chiral_restr 0.124 r_bond_refined_d 0.02 r_gen_planes_refined 0.008 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6420 Nucleic Acid Atoms Solvent Atoms 10 Heterogen Atoms
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction PHASER phasing